That takes more of a parser to keep track of state vis a vis quotes and escapes.
For just letters, numbers, dot and _:
Code:
sed '
s/[a-zA-Z0-9_.]\{1,99\}@[-a-zA-Z0-9.]*[a-zA-Z][-a-zA-Z0-9.]*/\
&\
/g
t
d
' your_file | fgrep '@' | sort -u
Narrative: Have sed put line feeds before and after any such email address found with the host containing with a letter in it, grep out any lines with at-sign and sort unique.
Last edited by DGPickett; 02-17-2012 at 06:00 PM..
I'm trying to answer the following question about file permissions in Unix. Consider a file with the following permissions:
rwx---r--
I am not the owner of this file, but I am a member of the group of this file.
My question is: do I have read access to this file?
I thought... (3 Replies)
Here's my problem:
I have a laptop running Windows XP Pro with no internal CD or Floppy drives. I want to install Linux on it. I don't care about the Windows XP Pro installation, in fact I would like to install Linux over the entirety of the HD. However I cannot boot from any external CD drive... (1 Reply)
Hi,
I'm in the midst of writing a UNIX script that sftp's files to an external host and am stuck with a problem. The problem is that the files created on my server as a order number that correlates to a sequence of directories on the remote host which is where the file should be ftp'ed.
... (3 Replies)
Hi,
I am at a point in my script where I defined the number of the command line parameter I would like to set a variable equal to:
parameter_number=14
I would then like to set a variable equal to the correct parameter:
variable=$parameter_number
The issue here is that {} is required... (2 Replies)
Hello everyone,
unfortunately I am no unix nor scripting guru, which is why I am asking for help here. I am trying to reformat a .csv file using sed or awk which has the following format:
a,b,C-D-E,f,g
h,i,J,k,l
m,n,O-P-Q-R-S,t,u
v,w,X-Y,z,a
It's basically a 5-field text file which has an... (7 Replies)
This post is in reference to https://www.unix.com/shell-programming-scripting/137977-tricky-sed-awk-question-post302428154.html#post302428154
I am trying to go the opposite direction now:
I have the following file:
a,b,C,f,g
a,b,D,f,g
a,b,E,f,g
h,i,J,k,l
m,n,O,t,u
m,n,P,t,u
m,n,Q,t,u... (3 Replies)
Hi folks!
My first post here.
I'm working on a script that retrieves a range of files from a list depending on a range of time.
UPDATE:
I've seen it could be difficult to read all this thing, so I'll make a summarize it..
How come I do this and take a result..
grep "..\:.." lista.new |... (4 Replies)
Hello,
i have this issue:
text="-8x7YTVNk2KiuY-PWG5zzzjB-zzw"
string=-8x7YTVNk2KiuY-PWG5zzzjB-zzw
echo $text | grep -v \'$string\'
-8x7YTVNk2KiuY-PWG5zzzjB-zzw
echo \'$string\'
'-8x7YTVNk2KiuY-PWG5zzzjB-zzw'
..and ofcourse if I do like this :
echo $text | grep -v $string
grep: invalid... (5 Replies)
Tricky one:
I want to do several things all at once to blow away a directory (rm -rf <dir>)
1) I want to find all files recursively that have a specific file extension (.ver) for example.
2) Then in that file, I want to grep for an expression ( "sp2" ) for example.
3) Then I want to... (1 Reply)
I have some data files that I can identify by a certain pattern in the names using find.
Every one of those data files has an XML file associated with it (can be multiple data files per XML file).
The XML file is always up one directory from the data file(s) in a folder calledRun##### -... (12 Replies)
Discussion started by: Michael Stora
12 Replies
LEARN ABOUT DEBIAN
bio::seqio::tab
Bio::SeqIO::tab(3pm) User Contributed Perl Documentation Bio::SeqIO::tab(3pm)NAME
Bio::SeqIO::tab - nearly raw sequence file input/output stream. Reads/writes id" "sequence"
"
SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
DESCRIPTION
This object can transform Bio::Seq objects to and from tabbed flat file databases.
It is very useful when doing large scale stuff using the Unix command line utilities (grep, sort, awk, sed, split, you name it). Imagine
that you have a format converter 'seqconvert' along the following lines:
my $in = Bio::SeqIO->newFh(-fh => *STDIN , '-format' => $from);
my $out = Bio::SeqIO->newFh(-fh=> *STDOUT, '-format' => $to);
print $out $_ while <$in>;
then you can very easily filter sequence files for duplicates as:
$ seqconvert < foo.fa -from fasta -to tab | sort -u |
seqconvert -from tab -to fasta > foo-unique.fa
Or grep [-v] for certain sequences with:
$ seqconvert < foo.fa -from fasta -to tab | grep -v '^S[a-z]*control' |
seqconvert -from tab -to fasta > foo-without-controls.fa
Or chop up a huge file with sequences into smaller chunks with:
$ seqconvert < all.fa -from fasta -to tab | split -l 10 - chunk-
$ for i in chunk-*; do seqconvert -from tab -to fasta < $i > $i.fa; done
# (this creates files chunk-aa.fa, chunk-ab.fa, ..., each containing 10
# sequences)
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHORS
Philip Lijnzaad, p.lijnzaad@med.uu.nl
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args :
write_seq
Title : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
perl v5.14.2 2012-03-02 Bio::SeqIO::tab(3pm)